Members of the L1 transposon family (long interspersed repeat DNA or LINE family) of rats are 6.7 kb long, 5 kb of which is devoted to two protein encoding genes. A transcriptional regulatory region is at the left end of the element, and a guanine-rich polypurine:polypyrimidine sequence is near the right end. Although the protein encoding sequences of mammalian L1 families are highly conserved, the promoter sequences are completely distinct. This means that these families have been independently amplified in various mammalian species. Our recent studies of an ancient L1 family as well as recently evolved clads of the modern rat L1 indicate that episodic L1 amplification has occurred repeatedly during mammalian evolution. We have also shown that analysis of an ancient amplification event can be a novel and powerful tool for determining phylogenetic relationships between modern animals. Our previous demonstration that the rat L1 family contains an active regulatory region was the first evidence that L1 DNA is not just some non-functional "junk" DNA. We have further characterized the L1 regulatory region and found that it contains three regions that can form specific DNA:protein complexes with nuclear proteins. Deletion analysis shows that one region binds a transcriptional stimulatory factor. We also have found that the L1 regulatory region activates both known and cryptic promoters located 5', but not 3', to it, in an orientation dependent manner. Therefore, the L1 regulatory region is not an "enhancer" sequence in the usual sense. We previously showed that the L1 guanine-rich polypurine:polypyrimidine sequence destabilizes contiguous duplex DNA, adopts several non-B DNA structures in vitro, and that the L1 non-B structures compete with target site non-B structures for supercoil energy which in vivo might modulate the supercoil dependent properties of L1 elements and their target sites. We now find that the L1 polypurine:polypyrimidine sequence decreases the replication of plasmids in both bacteria and mammalian cells and alters the apparent activity of certain eukaryotic promoters in vivo. In parallel studies we have shown that homoguanine stretches enhance the mutation and recombination rate of adjacent DNA sequences in vivo.